[gmx-users] Designing a topology file: bonded/non-bonded mess

David van der Spoel spoel at xray.bmc.uu.se
Sun Oct 14 13:50:32 CEST 2007

Frankie Montenegro wrote:
> Wow, I didn't realize you guys in Europe work 24/7 too. On Sunday morning
> nonetheless :-)
new on the list? (I know you're not...)
> On 10/14/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>> question: are there chemical bonds between "molecules" (which you seem
>> to imply by stating the sites are connected by an aromatic ring). If
>> there are then your whole system should be considered as a single
>> molecule. Have you tried x2top on this? (gmx 3.3.2 only).
> Yes they are. x2top wouldn't work, most atoms are redefined (two types
> of O with
> different charges, two types of C, etc. All are custom-fitted with
> Gaussians and GULP) I don't think treating the whole system as one
> molecule could work. A single "cell" of the crystall would have over
> 250 atoms, and I need 2x2 structure minimum, probably even bigger. But
> that might be last resort (after all , aren't some proteins over
> couple of thousand atoms?)

you can tune x2top as you see fit by editing the ffoplsaa.n2t file. Size 
is not a problem, and you can use periodic molecules as well.
Not sure what you're after, but I hope you realize that GROMACS can only 
do pair potentials, so no funky non-bonded three body potentials.

> BTW, what is the slope of GMX_performance vs. molecule_size curve ?
> There is one more regrouping that I am trying right now (namely having two
> moleculetypes: "cube-edge" and "cube-node", adding some  table "LJ" in between).
>  If this doesn't go, I am out of ideas.  Thanks anyway.
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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